Excess manure nutrients transported off livestock farms can produce adverse environmental and health effects. Subsurface nitrate attenuation is a set of ecosystem services that livestock farms can harness to reduce their nitrate emissions. However, the capacity of the subsurface environment to attenuate nitrates is commonly either neglected or considered as exogenous to farm management and policymaking. This study develops an integrated model for evaluating the role of nitrate attenuation in reducing nitrate emissions from concentrated animal feeding operations (CAFOs) and conducts a case study to explore policies that can encourage farmers to take advantage of this role. Four main conclusions arise. First, it is imperative to use integrated dynamic modeling to explore the best strategies and policies for managing nitrate emissions from CAFOs. Second, nitrate attenuation can play a significant role in reducing nitrate emissions from CAFOs. Third, to promote CAFOs to enhance nitrate attenuation for emission reduction, emission-based policies are preferred over input-based policies, in terms of both the efficacy and cost-effectiveness of the policies. Lastly, it is important for a policy design to consider the scales of pollution and to target emissions on a broader scale if possible.